import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
+ private boolean showAnnotation = true;
SequenceAnnotationOrder sortAnnotationsBy = null;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack<CommandI> historyList = new Stack<CommandI>();
- Stack redoList = new Stack();
+ Stack<CommandI> redoList = new Stack<CommandI>();
int thresholdTextColour = 0;
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
+ private boolean rightAlignIds = false;
/**
* Creates a new AlignViewport object.
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
*/
public boolean getShowAnnotation()
{
- return showAnnotation;
+ return isShowAnnotation();
}
/**
}
}
-<<<<<<< HEAD
+
public Hashtable getFeaturesDisplayed()
{
return featuresDisplayed;
public void setFeaturesDisplayed(Hashtable featuresDisplayed)
{
this.featuresDisplayed = featuresDisplayed;
-=======
+ }
protected SequenceAnnotationOrder getSortAnnotationsBy()
{
return sortAnnotationsBy;
protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
->>>>>>> branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalview.org/git/jalview.git
+ }
+
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
}
}